Journal of Computational Chemistry

The XYG3-type doubly hybrid (xDH) functionals are nonvariational in both the hybrid density functional part and the second-order perturbation part, each of which requires formally a coupled-perturbed Kohn–Sham equation to be solved for analytic gradients. An implementation is reported here which combines the two parts by defining a total Lagrangian such that only a single set of the Z-vector equations need to be solved. Test calculations are provided to demonstrate the satisfactory performance of the xDH functionals for geometry optimizations.

Accurate theoretical estimation of protein–ligand interaction is vitally important for the rational design of an effective drug. In this work, we have developed a nonfitting protein–ligand interaction scoring function based on divide and conquer strategy and first-principles methods. Good correlations on applications to cyclin-dependent kinase 2 and p21-activated kinase 1 inhibitor databases are found between the calculated scores and the experimental inhibitor efficacies with the square of correlation coefficient R² of 0.76–0.89.

O1s core-electron binding energies of electrophilic and nucleophilic oxygens important for olefin epoxidation on silver surface were investigated by the symmetry-adapted-cluster configuration-interaction (SAC-CI) method combined with the dipped adcluster model (DAM). The experimental information and our theoretical results indicate that Oelec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that Onuc is the one on the reconstructed added-row site of Ag(110).

A set of exchange-correlation functionals, including BLYP, PBE0, B3LYP, BHandHLYP, CAM-B3LYP, LC-BLYP, and HSE, has been used to determine static and dynamic nonresonant (nuclear relaxation) vibrational (hyper)polarizabilities for a series of polymethineimine oligomers containing up to eight monomer units. These functionals are assessed against reference values obtained using the MP2 and CCSD methods.

A newly developed HF-3c quantum chemical protocol combines a Hartree- Fock/small basis set calculation with three physically plausible atom-pair wise correction terms. It yields good results for non-covalent interactions, geometries of organic molecules, supramolecular complexes and small proteins. For most test cases its accuracy approaches DFT-D3/large basis set quality, but obtained at a tiny fraction of computational cost and can hence be applied to large molecular systems as an alternative to semiempirical methods.

The thiolate-ligated iron(IV)-oxo porphyrins, known as collectively as thiolate compound I, are potent and ubiquitous oxidizing agents active in both the cytochrome P450 superfamily of enzymes and in several highly reactive synthetic complexes. This particular species is characterized for the first time in a plane-wave density functional theory framework and benchmarked with respect to established localized-basis calculations.

The CH₂ system plays an important role in atmospheric and combustion chemistry, thus, to know clearly the chemically dynamical properties will be of great importance. For H(²S) + CH(X²Π) → C(¹D) + H₂(X¹), we presented the full information of reaction probability, integral cross section and rate constants, various angular distributions as well as the extracted polarization-dependent differential cross-sections. Both quasiclassical trajectory and time-dependent quantum wave-packet methods were carried out on BHL PES.

A simple molecular mechanics model for the non-heme Fe(II) site is developed and tested using molecular dynamics simulations for enzymes in the AlkB family. Although structural features for the ABH2-dsDNA complex are overall in good agreement with the crystal structure, the dsDNA and AlkB-dsDNA interface undergo substantial changes. The results highlight that crystal packing may have a significant impact on the structure of protein-DNA complexes and provide additional insights regarding substrate specificity of AlkB enzymes.

Presenting computational optimization methods that can predict protein secondary structures—α-helix and β-sheet—without any earlier knowledge, mimicking what occurs in nature, that is, using only interaction energy terms involved in the formation of protein structures. The proposed approach, called Multiobjective evolutionary algorithms with many tables (MEAMT), can perform a more adequate sampling of the objective space. MEAMT is an efficient optimization method for multiobjective optimization, which explores simultaneously the search space as well as the objective space.

A novel accurate potential energy surface and quantum wave packet dynamics calculations are reported for ground state of . The novel potential energy surface can both be recommended for dynamics studies of the reaction and as building blocks for constructing the DMBE/CBS potential energy surface of larger nitrogen/hydrogen-containing systems. In particular, this new surface can be using for studding the Renner–Teller degeneracy of the and states of .

We introduce a class of partial atomic charge assignment method that provides ab initio quality description of the electrostatics of bioorganic molecules. The method uses a set of models that neither have a fixed functional form nor require a fixed set of parameters, and therefore are capable of capturing the complexities of the charge distribution in great detail.

Knowledge about possible transition and reaction pathways is of utmost importance for the description of many processes like protein folding or complex enzymatic reactions. We propose a new algorithm based on a global optimization in a reduced phase space to locate possible transition states between reactants and products. Investigations for Ar₁₂ and Ar₁₃ underline the capability of the algorithm to find several reaction pathways in one shot.

Relative binding free energies of protein–ligand complexes formed by a focal adhesion kinase and various pyrrolopyrimidine-based compounds are calculated by means of steered molecular dynamics simulations. Nonequilibrium trajectories are analyzed using the Jarzynski equality for free energy calculations.

We present a new software package for simulation and inference of protein structure. The PHAISTOS framework contains a range of novel sampling techniques and probabilistic models, constituting a versatile toolkit for efficient simulations of protein structure. The package provides tools for a variety of tasks, including reversible folding simulations and probabilistic inference of protein structure from experimental data. The source code is released under an open source license, and full documentation is available online.

Iron Iron-sulfur proteins have finely tuned redox potentials, which allow them to be highly efficient and specific. Here, we derived bonded parameters compatible with the AMBER force field for three metal centers and performed molecular dynamics simulations on three proteins. Our results for the pattern of interactions with the metal centers are consistent to those obtained by NMR experiments and DFT density functional theory calculations, allowing the application of molecular dynamics to the study of those proteins.

Water cluster cations can have either the Eigen-like forms or the Zundel-like forms. Based on reliable molecular dynamics simulations, the water clusters tend to have an Eigen-like form with the hydronium cation instead of a Zundel-like form in terms of energetics. For the vertically ionized water hexamer, the relatively stable (H₂O)₅⁺ (5sL4A) cluster tends to form with a detached water molecule (H₂O).

Donor materials with different acceptor units for solar cells were designed and characterized through density functional theory calculations. It is found that 7 with naphthobisthiadiazole as acceptor fragment may become a high-performance donor due to broad- and red-shifted photoresponse, low exciton binding energies, high open-circuit voltage, and small reorganization energies.

Quantum chemical calculations using DFT (B3LYP), ab intio methods (MP2), and G2MP2 methods have been carried out to understand the preferences of tautomerization in medicinal relevant N-(pyridin-2-yl)thiazol-2-amine (PTA) scaffolds. PTA-P1 is the most preferred isomer for this class of compounds. It shows high proton affinity (∼235 kcal/mol) and gets converted into PTA-P1. Electronic structure analysis of PTA-P1 shows that this compound belongs to divalent N(I) of species; characterized by two lone pairs of electrons- π and σ type localized on the central nitrogen. Thus, the form PTA-P1 is labeled with (L→N←L)^⊕ character. © 2013 Wiley Periodicals, Inc.

An efficient fluctuating charge model for of transition metal complexes, based on the Hirshfeld partitioning scheme, has been developed and validated.

The lack of tools capable of predictive power in a high throughput fashion makes peptide global profiling quite challenging. To target this issue, a computational workflow was developed based on biophysical principles to predict the collision cross-section area of peptides as measured from ion mobility mass spectrometry experiments. Hosted on a web server, it allows the user to input a primary sequence (query) and retrieve information on peptide structure, sequence, and corresponding collision cross-section area.

Antimicrobial peptides are thought to kill bacteria by forming pores in their membranes but their selectivity towards bacterial membranes is not fully understood. An approach is developed to study binding of peptides to anionic membrane pores by combining the electrostatic potential obtained from solution of the Poisson–Boltzmann with the IMM1 implicit membrane model. The binding of two cationic peptides, magainin and melittin, to a pore displays different dependence on anionic content. This correlates with the observed selectivity of these peptides towards zwitterionic and anionic bilayers.

Molecular dynamics simulation reveals the effect of the Trp-Glu charge state on dipeptide conformation preferences. Two general conformations are found: one where the backbone stretches away from the indole ring, shown here. The consequence of a ‘backbone stretched’ conformation is noncovalent interaction between the terminal amine cation and indole ring, as illustrated here. Using this and other theoretical data, trends in tryptophan fluorescence maxima and lifetimes for different dipeptide species can be explained.

The precision of second hyperpolarizability calculations using the finite field approach can be refined combining the results of several different field strengths. Each entry of a column m is a linear combination of the two adjacent values from the m−1 column. Colored values indicate good precision. The reference value in atomic units is the second hyperpolarizability of neon at the HF/t-aug-cc-pVQZ level of theory.

It is shown how ab initio simulation can be used as a complementary tool for the interpretation of the experimental infrared reflectance spectra of solids. Accurate computed frequencies and intensities are an excellent guess for the best fit process used to extract the corresponding experimental quantities. Most of the symmetry allowed fundamental modes are in this way identified, including low intensity features. Combination modes are characterized, while artifacts due to background/noise are more easily disregarded.

Fullerene is an open-source general purpose program that constructs any fullerene graph, performs topological and physical analyses, and creates accurate 3D fullerene structures through graph theoretical methods and force-field optimizations. It allows for Goldberg–Coxeter transformations, vertex insertions, and Stone–Wales transformations.

Using robust local fitting procedures to approximate two-electron integrals, self-consistent field iterations may fail to converge as a result of effectively attractive electronic interactions. Convergence is recovered when the negative eigenvalues of the approximate two-electron integral matrix become sufficiently small. This is guaranteed when the auxiliary basis set is locally (near-) complete, which may be achieved using Cholesky-decomposition techniques.

The electronic and vibrational (hyper)polarizabilities of some rare gas derivatives, HXeOXeH, HXeOXeF, and FXeOXeF, are reported. All the studied properties were computed by employing state-of-the art quantum chemistry methods. This article discusses certain features associated with the remarkable effect of rare gas atom(s) on the electronic and vibrational nonlinear optical properties.

Equations needed to employ recent advances in orbital localization algorithms for the Pipek–Mezey (PM) localization function are presented, and used to investigate the locality of both occupied and virtual PM orbitals for large molecular systems. The locality of the occupied orbitals have seen to be generally good, although very system dependent (as displayed by picture of a occupied PM orbital for a graphene sheet plotted using contour 0.003). The virtual PM orbitals are shown to exhibit poor locality.

Making S-nitrosothiols click: CBS-QB3 calculations show that N-coordination of a Lewis acid (LA) is all that is necessary for S-nitrosothiols (RSNOs) to undergo efficient (3+2) cycloaddition reactions with activated alkynes or alkenes. We propose that LA-linked reagents may have great potential for labeling unstable protein-based RSNOs, as they are predicted to react with RSNOs with efficiency approaching click-chemistry based reactions.

The first high level quantum-chemical calculations of norbornadiene's singlet excited-state PE surfaces revealed a new photodeactivation path in which the dark doubly excited state has a prominent role due to the R₁/DE and DE/V₁ conical intersections.

The spectroscopy of magnetic circular dichroism has been lately profiting from the possibility to calculate accurately the spectra within the DFT and response theories. Surprisingly, we found that also the DFT sum over state path is a viable alternate approach, which under certain circumstances even significantly speeds up the spectral modeling.