Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations

The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated:  In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range.

Conformational analysis, part 43. A theoretical and LIS/NMR investigation of the conformations of substituted benzamides

A refined Lanthanide-Induced-Shift Analysis (LISA) is used with molecular mechanics and ab initio calculations to investigate the conformations of benzamide (1), N-methylbenzamide (2), N,N-dimethylbenzamide (3) and the conformational equilibria of 2-fluoro (4), 2-chloro (5) and N-methyl-2-methoxy benzamide (6). The amino group in 1 is planar in the crystal but is calculated to be pyramidal with the CO/phenyl torsional angle (ω) of 20-25°. The LISA analysis gave acceptable agreement factors (Rcryst ≤ 1%) for the ab initio geometries when ω was decreased to 0°, the other geometries were not as good. In 2, the N-methyl is coplanar with the carbonyl group in all the geometries. Good agreement was obtained for the RHF geometries, with ω 25°, the other geometries were only acceptable with increased values of ω. In 3, good agreement for the RHF and PCModel geometries was found when ω was changed from the calculated values of 40° (RHF) and 90° (PCModel) to ca. 60°, the X-ray and B3LYP geometries were not as good. The two substituted compounds 4, 5 and 6 are interconverting between the cis (O,X) and trans (O,X) conformers. The more stable trans conformer is planar in 4 and 6 but the cis form non-planar. Both the cis and trans conformers of 5 are non-planar. There is an additional degree of freedom in 6 due to the 2-methoxy group, which can be either planar or orthogonal to the phenyl ring in both conformers. The conformer ratios were obtained from the LISA analysis to give Ecis-Etrans in 4 > 2.3 kcal/mol (CDCl3 ) and 1.7 kcal/mol (CD3 CN), in 5 0.0 kcal/mol (CD3 CN) and in 6 > 2.5 kcal/mol (CDCl3 ) and 2.0 kcal/mol (CD3 CN). These values were used with the observed versus calculated (1) H shifts to determine the conformer ratios and energies in DMSO solvent to give Ecis-Etrans 1.1, -0.1 and 1.8 kcal/mol for (4), (5) and (6). Comparison of the observed versus calculated conformer energies show that both the MM and ab initio calculations overestimate the NH..F hydrogen bond in (4) by ca. 2 kcal/mol.

Conformational properties of cis- and trans-N-Cyclopropylformamide studied by microwave spectroscopy and quantum chemical calculations

The microwave spectra of cis- and trans-N-cyclopropylformamide, C3H5NHC(═O)H, have been investigated in the 31-123 GHz spectral region at room temperature. Rotational isomerism about the Cring-N bond is possible for both cis and trans. MP2/cc-pVTZ and CCSD/cc-pVTZ calculations indicate that there are two conformers in the case of cis, called Cis I and Cis II, while only one rotamer, denoted Trans, exists for trans-N-cyclopropylformamide. The quantum chemical methods predict that Cis I has an electronic energy that is 8-9 kJ/mol higher than the energy of Cis II. The CCSD H-Cring-N-H dihedral angle is 0.0° in Cis I, 93.0° in Cis II and 79.9° in Trans. The CCSD and MP2 calculations predict a slightly nonplanar structure for the amide moiety in both Trans and Cis II, whereas Cis I is computed to have a planar amide group bisecting the cyclopropyl ring. Surprisingly, the MP2 and CCSD methods predict practically the same energy for Trans and Cis II. The spectra of Cis II in the ground state and in two vibrationally excited states were assigned, while the spectrum of Cis I was not found presumably because of a low Boltzmann population due to a relatively large energy difference (8-9 kJ/mol). The spectra of the ground vibrational state and seven vibrationally excited states of Trans, were assigned. Vibrational frequencies of several of the excited state of both Cis II and Trans were determined by relative intensity measurements. The experimental and CCSD rotational constants are in satisfactory agreement. The MP2 values of the quartic centrifugal distortion constants of both species are in relatively poor agreement with their experimental counterparts. The MP2 vibration-rotation constants and sextic centrifugal distortion constants have little resemblance with the corresponding experimental values.

Vibronic structure in the far-UV electronic circular dichroism spectra of proteins

The Franck–Condon effect is considered and the vibrational structure of the π_nbπ* transition of the peptide backbone is incorporated into matrix method calculations of the electronic circular dichroism (CD) spectra of proteins in the far-ultraviolet. We employ the state-averaged CASPT2 method to calculate the ground and π_nbπ* excited state geometries and frequencies of N-methylacetamide (NMA), which represents the peptide chromophore. The results of these calculations are used to incorporate vibronic levels of the excited states into the matrix method calculation. The CD spectra of a set of 49 proteins, comprising a range of structural types, are calculated to assess the influence of the vibrational structure. The calculated spectra of α-helical proteins are better resolved using the vibronic parameters and correlation between the experimental and the calculated intensity of less regular β structure proteins improves over most wavelengths in the far-UV. No obvious improvement is observed in the calculated spectra of regular β-sheet proteins. Our high-level ab initio calculations of the vibronic structure of the π_nbπ* transition in NMA have provided some further insight into the physical origins of the nature of protein CD spectra in the far-UV.

All-atom empirical potential for molecular modeling and dynamics studies of proteins

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent-solvent, solvent-solute, and solute-solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volumes, and crystal pressures and structures were used in the optimization. The resulting protein parameters were tested by applying them to noncyclic tripeptide crystals, cyclic peptide crystals, and the proteins crambin, bovine pancreatic trypsin inhibitor, and carbonmonoxy myoglobin in vacuo and in crystals. A detailed analysis of the relationship between the alanine dipeptide potential energy surface and calculated protein φ, χ angles was made and used in optimizing the peptide group torsional parameters. The results demonstrate that use of ab initio structural and energetic data by themselves are not sufficient to obtain an adequate backbone representation for peptides and proteins in solution and in crystals. Extensive comparisons between molecular dynamics simulations and experimental data for polypeptides and proteins were performed for both structural and dynamic properties. Energy minimization and dynamics simulations for crystals demonstrate that the latter are needed to obtain meaningful comparisons with experimental crystal structures. The presented parameters, in combination with the previously published CHARMM all-atom parameters for nucleic acids and lipids, provide a consistent set for condensed-phase simulations of a wide variety of molecules of biological interest.

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.

1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group

The (1)H spectra of 37 amides in CDCl(3) solvent were analysed and the chemical shifts obtained. The molecular geometries and conformational analysis of these amides were considered in detail. The NMR spectral assignments are of interest, e.g. the assignments of the formamide NH(2) protons reverse in going from CDCl(3) to more polar solvents. The substituent chemical shifts of the amide group in both aliphatic and aromatic amides were analysed using an approach based on neural network data for near (≤3 bonds removed) protons and the electric field, magnetic anisotropy, steric and for aromatic systems π effects of the amide group for more distant protons. The electric field is calculated from the partial atomic charges on the N.C═O atoms of the amide group. The magnetic anisotropy of the carbonyl group was reproduced with the asymmetric magnetic anisotropy acting at the midpoint of the carbonyl bond. The values of the anisotropies Δχ(parl) and Δχ(perp) were for the aliphatic amides 10.53 and -23.67 (×10(-6) Å(3)/molecule) and for the aromatic amides 2.12 and -10.43 (×10(-6) Å(3)/molecule). The nitrogen anisotropy was 7.62 (×10(-6) Å(3)/molecule). These values are compared with previous literature values. The (1)H chemical shifts were calculated from the semi-empirical approach and also by gauge-independent atomic orbital calculations with the density functional theory method and B3LYP/6-31G(++) (d,p) basis set. The semi-empirical approach gave good agreement with root mean square error of 0.081 ppm for the data set of 280 entries. The gauge-independent atomic orbital approach was generally acceptable, but significant errors (ca. 1 ppm) were found for the NH and CHO protons and also for some other protons.

On potential energy models for EA-based ab initio protein structure prediction

Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.

Molecular dynamics simulations of N-methylacetamide (NMA) in water by the ABEEM/MM model

The N-methylacetamide (NMA) is a very interesting kind of compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of peptides in aqueous solutions. We have carried out molecular dynamics (MD) simulations of a NMA molecule in water under 1 atm and 298 K. The simulations make use of the newly developed NMA–water fluctuating charge ABEEM/MM potential model ( Yang, Z. Z.; Qian, P. J. Chem. Phys. 2006, 125, 064311 ), which is based on the combination of the atom-bond electronegativity equalization method (ABEEM) and molecular mechanics (MM). This model has been successfully applied to NMA–water gas clusters, NMA(H2O)n (n = 1–6), and accurately reproduced many static properties. For the NMA–water ABEEM/MM potential model, two characters must be emphasized in the simulations. Firstly, the model allows the charges in system to fluctuate, responding to the ambient environment. Secondly, for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters klpO=,H and klpO–,HN–, respectively, which explicitly describe the short-range interaction of hydrogen bonds in the hydrogen bond interaction region. All sorts of properties have been studied in detail, such as, radial distribution function, energy distribution, ABEEM charge distribution and dipole moment, and so on. These simulation results show that the ABEEM/MM-based NMA–water potential model appears to be robust, giving the solution properties in excellent agreement with other dynamics simulations on similar systems.

Switching in of Ac-(Ala)10-NHMe at a solid surface

Using molecular simulation, we show how Ac-(Ala)(10)-NHMe adsorbed on a solid surface switches between three conformations at distinct surface energies. The first switch is from an alpha-helix to a 3.1(10)-helix. The second involves further stretching to a 2(7)-helix. This switching has several potential applications including memory in molecular computers to motility elements in nanotechnology, and could be relevant to biological activity of proteins near solid surfaces (e.g., nano and aerosol particles) and disease processes induced by such interactions.

Geometry and Excitation Energy Fluctuations of NMA in Aqueous Solution with CHARMM, AMBER, OPLS, and GROMOS Force Fields: Implications for Protein Ultraviolet Spectra Simulation

Molecular dynamics (MD) simulations are performed for N-methylamide (NMA) in water at 300 K with different force fields. Compared to the three all-atom force fields (CHARMM22, AMBER03, and OPLS-AA), the united-atom force field (GROMOS96) predicts a broader distribution of the peptide OCNH dehedral angle. A map constructed by fitting the npi* and pipi* transition energies as quadratic functions of the NMA geometric variables is used to simulate the excitation energy fluctuations. GROMOS96 predicts blue-shifted npi* and pipi* energies and stronger fluctuations compared to the other three force fields, which indicates that different force fields may predict different spectral lineshapes for proteins.

X-ray scattering and density-functional theory calculations to study the presence of hydrogen-bonded clusters in liquid N-methylacetamide

A structural investigation of liquid N-methylacetamide (NMA) is performed by x-ray scattering and density functional theory (DFT). Experimental data are analyzed to yield the total structure function SM(Q) and the pair correlation function g(r). The DFT calculations, using the standard triple zeta valence basis set augmented by a diffuse function for carbon, nitrogen and oxygen atoms, are performed on the one hand to study the structure and stability of the two possible conformers cis and trans. On the other hand, they are meant to examine some possible clusters which may describe the intermolecular arrangement in liquid NMA. Among two series of dimers and trimers associations, the spectra are particularly interpreted in terms of: Trans NMA dimers and trimers which resemble the short-range crystal structure, mixed cis and trans trimers and cis cyclic trimers. The H-bonding parameters and the intermolecular energy for each model are described.

Local Order in Fully Deuterated Liquid N-Methylacetamide (C3D7NO) As Studied by Neutron Diffraction and Density-Functional Theory Calculations

A structural investigation of fully deuterated liquid N-methylacetmide (NMAd7) is performed at 308 K and atmospheric pressure by using neutron diffraction together with density-functional theory (DFT). The analysis of experimental data yields the total structure factor SM(Q), the molecular form factor F1(Q), and the distinct pair correlation function gL(r). The DFT calculations are performed to study the relative stability of the two possible isomers (trans and cis) and to examine some possible clusters recently published that may describe the intermolecular arrangement in the liquid state. Neutron measurements can be interpreted in terms of trans linear trimer (T1) and cis cyclic trimer (T2) where the total number of hydrogen bonds is respectively equal to two and three. The theoretical structure factors obtained on the basis of intermolecular arrangements agree fairly well with the experimental one beyond Q = 2 A-1. All through the study, a comparison is made with complementary X-ray results.

A study of N-methylacetamide in water clusters: Based on atom-bond electronegativity equalization method fused into molecular mechanics

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.

How to Model Solvation of Peptides? Insights from a Quantum-mechanical and Molecular Dynamics Study ofN-Methylacetamide. 1. Geometries, Infrared, and Ultraviolet Spectra in Water

This paper represents the first part of a study of solvation in peptides using quantum-mechanical and classical approaches. In this study, the peptide is modeled as its simplest analogue, namely, N-methyl-acetamide, and the effects of the solvent (here water, and in the second part of the study, water and acetone) are introduced at three different levels, e.g., through a continuum description, using solute-solvent clusters, and using the same clusters embedded in an external continuum. In turn, the solute-solvent clusters have been obtained in two alternative ways, either by using QM optimization procedures or extracting a proper set of structures from MD simulations. In this part of the study, geometries, IR, and UV spectra are calculated in terms of the different solvation models, and the results are analyzed and compared to get insights about different aspects of solvation involving dynamic and static effects on one hand and bulk or specific interactions on the other hand.

Neutron scattering study of the H-bond network in amorphous N-methylformamide

Original investigations of structural properties in noncrystalline solid N-methylformamide (HCONHCH(3)) are presented in this paper. After description of the sample preparation, the elastic neutron scattering formalism is applied to deduce the coherent scattering cross section for amorphous N-methylformamide. The contribution of each possible monomer (cis or trans) is computed and the corresponding distinct structure factor is deduced. Our measurements clearly show that the hydrogen-bond network occurs in amorphous N-methylformamide between C=O and N-H groups. The experimental spectra are consistent with an open-chain structure similar to the one existing in the crystalline form. The more probable clusters that have been identified in the liquid are also examined.

Intermolecular association in liquidN-methylacetamide as studied by x-ray scattering

A structural investigation of liquid N methylacetamide was performed at 308 K using x-ray scattering. To extract the molecular form factor F1(q), the geometry of the conformer which has been found in the crystal is considered. The intermolecular structure function DM(q) is interpreted in terms of H-bonding interactions. The crystal N...O distance is taken into accounted and the number of H bond(s) is assumed to be, respectively, equal to one and two. The liquid structure can be described by a linear dimer or chainlike trimer similar to the ones existing in the crystal. The structure factors SM(q) extracted from these clusters fairly agree with the experimental one beyond q=2.5 A(-1).

Empirical force fields for biological macromolecules: overview and issues

Empirical force field-based studies of biological macromolecules are becoming a common tool for investigating their structure-activity relationships at an atomic level of detail. Such studies facilitate interpretation of experimental data and allow for information not readily accessible to experimental methods to be obtained. A large part of the success of empirical force field-based methods is the quality of the force fields combined with the algorithmic advances that allow for more accurate reproduction of experimental observables. Presented is an overview of the issues associated with the development and application of empirical force fields to biomolecular systems. This is followed by a summary of the force fields commonly applied to the different classes of biomolecules; proteins, nucleic acids, lipids, and carbohydrates. In addition, issues associated with computational studies on "heterogeneous" biomolecular systems and the transferability of force fields to a wide range of organic molecules of pharmacological interest are discussed.